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Soil health

How can soil be healthy? Isn't it mostly just dead stuff and minerals?
Soil is alive with all sorts of life forms.

Stop and think! You are standing on the roof of a parallel soil world populated by more species of animals and plants than you will ever see above ground even in the rain forests of the Amazon. They are small, mostly microscopic in size and many are yet to be identified and named. Were they all extracted from the soil and put on a giant set of scales, the soil organisms from a single hectare of arable soil would weigh 5 tonnes, same as 100 full grown sheep. In just one handful of fertile soil, there can be 100 billion bacteria and 50 kilometres of fungal filament.

British Society of Soil Science

A quarter* of the total biodiversity of the planet is found in soils, according to the Encyclopedia of the Environment, 2022

*Update August 2023: More recent research suggests that 50% is closer to the mark. More than half of Earth’s species live in the soil, study finds

Highly recommended that you download a free .pdf copy of Global Soil Biodiversity Atlas from

It will fill in lots of detail for you, especially about soil biota. It also has a very useful glossary for unfamiliar terms.

Organisms in soil

Soil organisms have very important roles in soil health

  • decomposing organic matter thus making new materials available to above ground plants
  • improving and maintaining soil structure
  • mixing organic matter through the soil
  • controlling populations of pathogens
  • degrading pollutants

Soil fauna

handful of soil with earthworms

Most of us would be familiar with this soil dweller, the earthworm, but how about we check out some of its neighbours?

Most animals are in the top layers of soil, usually the top few centimetres, because this is usually where most of the organic matter is concentrated. There is a very high diversity among soil animals. They can be roughly sorted into 4 categories

GroupingSize Range (mm)Examples
megafauna>20burrowing mammals such as moles, some species of earthworm,
macrofauna2 to 20nematodes, mites, springtails, spiders, insects, and some species of earthworms
mesofauna0.2 to 2mites, spring tails, nematodes nematodes, rotifers, tardigrades, small araneidae, pseudoscorpions, opiliones, enchytraeids, insect larvae, small isopods and myriapods.
microfauna0.02 to 0.2protozoa, small mites, nematodes, rotifers, tardigrades and copepod crustaceans all fall within the upper limit.

Video examples of soil fauna

Microbes in the soil


Fungi are primarily organisms that cannot synthesise their own food and are can be unicellular (e.g. yeasts) or multicellular (most other fungi). Multicellular fungi are built up of threads called hyphae.

The great majority of fungal species recorded so far are likely to spend at least some portion of their life cycle in soil. Soil fungi have fundamental ecological roles as decomposers, mutualists, or pathogens of plants and animals. Fungi drive soil carbon cycling and mediate mineral nutrition of plants in both natural and anthropogenic ecosystems. As fungi are heterotrophs that rely on photosynthetic carbon as their source of food, both direct and indirect interactions with plants are an important part of fungal ecology.

Some fungi are saprophytic - they digest dead plant and animal remains by breaking them down with enzymes and taking in the resultant compounds. Others have are parasitic on living organisms. Others have more complex ways of obtaining nutrition -one of the most studied plant root/fungus interactions is the mycorrhizal symbiosis.

For an understanding of this vitally important topic, please see this case study in one of my other sites -

Most fungi are only noticed by humans once their fruiting bodies (commonly called mushrooms and toadstools) emerge from the soil.


algae on soil surface
algae on soil surface

Algae are photosynthesis capable organisms which can live in the upper reaches of the soil where light is present. The soils are home to about 170 genera with ca. 1000 species of eukaryotic algae. The formation of algal crusts on the soil interferes with soil erosion, increases rainwater storage and reduces water loss by evaporation during dry periods.


lichen on soil
lichen on soil

Lichens, or lichenised fungi, are organisms made up of a fungus and one or more algae or a cyanobacterium in a symbiotic relationship.

Lichens are able to fix atmospheric nitrogen which becomes available through leaching or decay and can be a significant source of nitrogen for plants. Lichens also absorb mineral nutrients, are a source of food for animals, provide habitat for invertebrates and can create soil crusts which control erosion and protect soil structures in semi-arid and arid lands.


soil bacteria types
types of soil bacteria

Most bacteria in soil are about 1/1000 of a millimetre in length or diameter. Their size varies with their environment. Bacteria in environments that have high levels of nutrients may be larger than those in nutrient poor conditions.

The majority of bacteria in soil usually occur as single cells. Bacteria sometimes join together in chains or clusters. They mainly have one of two shapes - spheres (called cocci) and rods (called bacilli).

They are important biochemical agents in the soil, intimately connected to decomposition and recycling of minerals.

Bacteria live in the water-filled pore spaces within and between soil aggregates. As such, their activities are directly dependent on how much soil water is available. They are normally found on the surfaces of mineral or organic particles or congregate around particles of decaying plant and animal debris. Most are unable to move of their own accord, so their dispersion is dependent on water movement, root growth or the movement of soil aggregates, or of other organisms.

Cyanobacteria (often erroneously called bluegreen algae) are a group of photosynthetic bacteria widely distributed in aquatic habitats and terrestrial habitats (e.g. moist soils). They may live singly or in colonies (by forming filaments or spheres with other cyanobacteria). Cyanobacteria are important oxygen producers of the planet. Some of them can fix atmospheric nitrogen, which can then be used to feed plants. The contribution of nitrogen-fixing cyanobacteria to the soil nitrogen pool can reach 30 kg/ha

Cyanobacteria in the soil are particularly valuable as components of biocrusts.  Biological soil crusts are communities of living organisms on the soil surface in arid and semi-arid ecosystems. These biocrusts form at the uppermost millimeters of soil and are an aggregation of minerals and microorganisms. In dryland regions, biocrusts can cover up to 70% of the land surface area, and overall , covering about 12% of Earth’s terrestrial surface They are important protectors against erosion from winds in these areas.


Actinomycetes  are the most abundant organisms that form thread-like filaments in the soil and are responsible for characteristically “earthy” smell of freshly turned healthy soil. They play major roles in the cycling of organic matter; inhibit the growth of several plant pathogens and decompose complex compounds in dead plant, animal and fungal material results in production of many extracellular enzymes which are conductive to crop production. They contribute to pH regulation of soils, biological control of soil environments by nitrogen fixation and degradation of high molecular weight compounds like hydrocarbons in the polluted soils are remarkable characteristics of actinomycetes. Besides this, they are known to improve the availability of nutrients, minerals, enhance the production of metabolites and promote plant growth regulators.

Streptomyces, which is associated with many of the antibiotics we use in medical treatment is a genus in the Actinomycetes group.


Viruses are tiny, even in comparison to bacteria. Typical size range for viruses is about 20 to 200 millionths of a millimeter. If a virus were the size of a flea, a corresponding person would be the size of Mount Everest!

They consist of packets of DNA or RNA genetic material inside a protein coat, sometimes contained within a lipid envelope. Viruses are parasites, in that they rely on host cell machinery for replication. A free viral particle is biologically inert/unalive and subject to biological and environmental degradation.

virus compared to bacterium

Most of the soil viruses are thought to be bacteriophages - viruses that attack bacteria and hijack the bacteria's biochemical processes to create new viruses. They are thought to be superabundant in soils with a high water content, and less so in dry sandy type soils.

The field of soil virology is not as yet well researched.

Soil food webs

It makes it easier to understand the organisms in soil by examining their groupings, but it is their interaction that is critical to the functioning of soil. Various combinations of the organisms mentioned above are linked together by examining their feeding relationships and therefore energy flow, Here are some visual interpretations of soil food webs.

For any given locale, the species of organism involved will vary due to climate and soil type, but the general pattern (as shown in the boxes at the bottom of the 4th image) is the very similar all over.

Examples of interaction outside the food web

  • Soil biota are important in the process of aggregation of mineral and organic particles into solid structures by producing polysaccharides, which glue particles together. Fungi participate in aggregation processes also by entangling particles into ‘nets’ of fungal filaments.
  • Earthworms and other burrowing organisms provide channels for water to penetrate the soil to allow water to penetrate more easily and therefore make it available to other smaller organisms.

In healthy soils, the main roles that soil organisms (both invertebrate animals and microbes) perform -

  • Decompose organic residues
  • Re-cycle nutrients from organic residues
  • Modify soil structure
  • Soil organisms degrade chemicals and pollutants that enter soil
  • Some soil organisms live in mutually beneficial relationships with plants, enhancing the plant’s nutrition by increasing the nitrogen uptake from the atmosphere via bacterial action or phosphorus uptake from the soil by soil  through mycorrhizae

Getting your hands dirty

Go to Explore my understanding of Soil Health

Click on the following link to visit the page - Explore my understanding of Soil -Health (will open in a new window or tab)

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